If FileBot does not automatically match the correct Episode or Movie for any given file, then you can manually select the correct Episode (or multiple episodes for multi-episode files) or Movie instead via Double-Click ➔ Edit Match.
You can select multiple episodes if the file at hand is a multi-episode file:
(requires FileBot r9301) You can prefabricate double-episode / triple-episode / multi-episode objects for manual matching en masse in the Episodes tool: